rs2865591

Variant names:

• chr2-57209689-T-C
• rs2865591

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.233 in 151,950 control chromosomes in the GnomAD database, including 4,559 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4559 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35479 AN: 151832 Hom.: 4559 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.252

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 35478 AN: 151950 Hom.: 4559 Cov.: 32 AF XY: 0.236 AC XY: 17546 AN XY: 74264

African (AFR) AF: 0.131 AC: 5418 AN: 41488

American (AMR) AF: 0.294 AC: 4483 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3472

East Asian (EAS) AF: 0.137 AC: 710 AN: 5166

South Asian (SAS) AF: 0.191 AC: 917 AN: 4812

European-Finnish (FIN) AF: 0.326 AC: 3437 AN: 10542

Middle Eastern (MID) AF: 0.221 AC: 64 AN: 290

European-Non Finnish (NFE) AF: 0.278 AC: 18888 AN: 67890

Other (OTH) AF: 0.249 AC: 526 AN: 2112

Alfa AF: 0.257 Hom.: 667

Bravo AF: 0.227

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.52
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2865591; hg19: chr2-57436824;